This codecheck was done as part of the “CodeCheck goes NL” workshop in Erasmus University Rotterdam, The Netherlands. The codechek process was carried out in two stages. During the workshop, the reproduction of Figure 5 in the manuscript was achieved with help from the authors. Following the workshop, the authors provided the codecheckers with a Jupyter notebook capable of generating most of the figures presented in the manuscript, along with those in the supplementary materials.
The authors have made available the necessary code and data to reproduce the figures and tables in the manuscript and supplementary documentation. These resources can be accessed at https://osf.io/y2q3r/.
Figure 5 was reproduced by running the Jupyter notebook
Empatica.ipynb(https://osf.io/7h48c). The authors assisted the
codecheckers in fixing minor issues in the code, mainly related to
incorrect paths to the data files needed to generate the plot. The
following changes were made to the code:
path variable in the notebook’s second
cell; its value was set to
<local-path>/osfstorage-archive/Raw Data/Empatica Avro Filesevents_path variable the fourth cell; its
value was set to
<local-path>/osfstorage-archive/Raw Data/" + pp + "_events.csvAll the necessary libraries to run the notebooks, except for Jupyter
itself, were obtained by installing the wearablehrv package
as documented in the README file of the repository https://github.com/Aminsinichi/wearable-hrv.
Following the workshop, the authors uploaded to the article’s OSF
project the Jupyter notebook
Quality in Question - Reproduce Results.ipynb (https://osf.io/x6t5n) which
was used by the codecheckers to reproduce all the other figures and
tables included in this report.
The codechekers suggest to the authors to consider the following suggestions for their next publication or workflow:
os.path.join to handle the paths in
Python codeComment: manuscript Fig. 2 (empatica)
Comment: manuscript Fig. 2 (heartmath)
Comment: manuscript Fig. 2 (kyto)
Comment: manuscript Fig. 2 (rhythm)
Comment: manuscript Fig. 4 (mean hr)
Comment: manuscript Fig. 4 (rmssd)
Comment: manuscript Fig. 5
Comment: manuscript Fig. 6 (arithmetic, meanhr)
Comment: manuscript Fig. 6 (arithmetic, rmssd)
Comment: manuscript Fig. 6 (biking, mean hr)
Comment: manuscript Fig. 6 (biking, rmssd)
Comment: manuscript Fig. 6 (sitting, mean hr)
Comment: manuscript Fig. 6 (sitting, rmssd)
Comment: manuscript Fig. 7 (mean hr)
Comment: manuscript Fig. 7 (rmssd)
Comment: manuscript Fig. 8 (mean hr)
Comment: manuscript Fig. 8 (rmssd)
Comment: manuscript Fig. 9 (arithmetic, meanhr)
Comment: manuscript Fig. 9 (arithmetic, rmssd)
Comment: manuscript Fig. 9 (biking, mean hr)
Comment: manuscript Fig. 9 (biking, rmssd)
Comment: manuscript Fig. 9 (sitting, mean hr)
Comment: manuscript Fig. 9 (sitting, rmssd)
Comment: manuscript Table 1
Comment: supplement Fig. 4 (empatica)
Comment: supplement Fig. 4 (heartmath)
Comment: supplement Fig. 4 (kyto)
Comment: supplement Fig. 4 (rhythm)
Comment: supplement Fig. 5 (empatica)
Comment: supplement Fig. 5 (heartmath)
Comment: supplement Fig. 5 (kyto)
Comment: supplement Fig. 5 (rhythm)
Comment: supplement Fig. 6 (empatica)
Comment: supplement Fig. 6 (heartmath)
Comment: supplement Fig. 6 (kyto)
Comment: supplement Fig. 6 (rhythm)
Comment: supplement Fig. 7 (kyto)
Comment: supplement Fig. 7 (rhythm)
Comment: supplement Fig. 8 (empatica)
Comment: supplement Fig. 8 (heartmath)
Comment: supplement Fig. 9 (kyto)
Comment: supplement Fig. 9 (rhythm)
Comment: supplement Table 3
Comment: supplement Table 4
Comment: supplement Table 5
We would like to acknowledge NWO for funding the CHECK-NL project, and enabling the workshop at Rotterdam.
Yasel Quintero, Tornike Skhirtladze, Joslyn Sun, Gabriella Low Chew Tung, Roel Janssen (2024). CODECHECK Certificate 2024-019. Zenodo. https://doi.org/10.5281/zenodo.FIXME
This certificate confirms that the codecheckers could independently reproduce the results of a computational analysis given the data and code from a third party. A CODECHECK does not check whether the original computation analysis is correct. However, as all materials required for the reproduction are freely available by following the links in this document, the reader can then study for themselves the code and data.
This document was created using R Markdown using the codecheck
R package. make codecheck.pdf will regenerate the report
file.
sessionInfo()
## R version 4.4.1 (2024-06-14)
## Platform: aarch64-apple-darwin20
## Running under: macOS 15.1.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
##
## locale:
## [1] C/UTF-8/C/C/C/C
##
## time zone: Europe/Amsterdam
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets
## [6] methods base
##
## other attached packages:
## [1] readr_2.1.5 tibble_3.2.1 xtable_1.8-4
## [4] yaml_2.3.10 rprojroot_2.0.4 knitr_1.49
## [7] codecheck_0.11.4 parsedate_1.3.1 R.cache_0.16.0
## [10] gh_1.4.1
##
## loaded via a namespace (and not attached):
## [1] xfun_0.49 bslib_0.8.0 rdflib_0.2.9
## [4] tzdb_0.4.0 vctrs_0.6.5 tools_4.4.1
## [7] generics_0.1.3 parallel_4.4.1 curl_6.0.1
## [10] fansi_1.0.6 pkgconfig_2.0.3 pdftools_3.4.1
## [13] R.oo_1.27.0 redland_1.0.17-18 assertthat_0.2.1
## [16] lifecycle_1.0.4 compiler_4.4.1 atom4R_0.3-3
## [19] stringr_1.5.1 keyring_1.3.2 htmltools_0.5.8.1
## [22] sass_0.4.9 pillar_1.9.0 crayon_1.5.3
## [25] jquerylib_0.1.4 whisker_0.4.1 tidyr_1.3.1
## [28] R.utils_2.12.3 cachem_1.1.0 zen4R_0.10
## [31] tidyselect_1.2.1 zip_2.3.1 digest_0.6.37
## [34] stringi_1.8.4 dplyr_1.1.4 purrr_1.0.2
## [37] fastmap_1.2.0 cli_3.6.3 magrittr_2.0.3
## [40] XML_3.99-0.17 crul_1.5.0 utf8_1.2.4
## [43] withr_3.0.2 osfr_0.2.9 bit64_4.5.2
## [46] roxygen2_7.3.2 rmarkdown_2.29 httr_1.4.7
## [49] bit_4.5.0 qpdf_1.3.4 askpass_1.2.1
## [52] R.methodsS3_1.8.2 hms_1.1.3 memoise_2.0.1
## [55] evaluate_1.0.1 rlang_1.1.4 Rcpp_1.0.13-1
## [58] glue_1.8.0 httpcode_0.3.0 xml2_1.3.6
## [61] fauxpas_0.5.2 rorcid_0.7.0 vroom_1.6.5
## [64] jsonlite_1.8.9 plyr_1.8.9 R6_2.5.1
## [67] fs_1.6.5